NAMD

NAMD is a parallel molecular dynamics code based on Charm++ designed for high-performance simulation of large biomolecular systems.

Licensing Terms and Conditions

ALPS (GH200)

You can obtain NAMD's Spack stack as follows

# List available images
uenv image find namd

# Pull the image of interest
uenv image pull namd/3.0b6:latest

# Start uenv (with namd view, providing the namd3 executable)
uenv start --view=namd namd/3.0:v3

NAMD and its main dependencies are conveniently provided as modules. If you prefer to use modules instead of the namd  view, you can do the following instead to start the environment

uenv start --view=modules namd/3.0:v3

in order to have the NAMD executable available.

Single-node, single- or multi-GPU

The single-node build works on a single node and benefits from the new GPU-resident mode (see NAMD 3.0b6 GPU-Resident benchmarking results for more details).

srun -N 1 -n 1 --gres=gpu:4 namd3 +p 8 +setcpuaffinity +devices 0 stmv_gpures_nve.namd
srun -N 1 -n 1 --gres=gpu:4 namd3 +p 15 +pmepes 7 +setcpuaffinity +devices 0,1 stmv_gpures_nve.namd
srun -N 1 -n 1 --gres=gpu:4 namd3 +p 29 +pmepes 5 +setcpuaffinity +devices 0,1,2,3 stmv_gpures_nve.namd

Scaling of the tobacco mosaic virus (STMV) benchmark with GPU-resident mode on our system is the following:

The official NAMD 3.0b6 GPU-Resident benchmarking results provide results for A100 GPUs as well as the older GPU-offload mode. The following graphs compares results on A100 (official benchmarks) and GH200 (our results) for both GPU-resident and GPU-offload modes.

Further Documentation

NAMD Homepage

NAMD User's Guide